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I know this is an old post, but seeing how many views it has received I figured I would provide some potentially helpful information. I also had water accumulation in the driver's side passenger foot area of my 2004 XJ8. I first cleaned out the drains, then removed the headliner, then sealed the panel gaps and chased all other posted information including in the TSBs. No luck.

I finally found the problem. Above the doors starting at the hood and running to the trunk above the doors is a chrome trim strip. Behind the chrome trim stip, both top and bottom are two - two piece rubber seals. The longest pieces run from the hood to 2/3 the way through the rear door (both top and bottom). From there two smaller strips run, both top and bottom the rest of the way. What I found is a gap on both the top and bottom rubber seals. This permitted water flowing down the chrome strip drain channel path the ability to enter the cabin. Using the passenger side as a reference I deduced how the factory originally positioned the seals. Mine had moved foward about 1/2 to 3/4 an inch. After trying to push the rubber seal it would not move due to friction. I used a credit card between the body and seal to dislodge any places it was sticking - no glue is involved and the seal is free to move by design. Starting at the front I wedged the credit card in and ran it the length of the seal. Then I slowly worked back and forth moving the seal back to where it originally resided. It takes some time. I used a tweezers to pull when my fingers did not work, making sure not to scratch anything or damage the rubber seal. I used this technique for both top and bottom until the seals were back in place. It sounds more difficult than it really is - basically you are just pulling the rubber back into their original position.

I originally thought of pulling the chrome strip, but it would not budge and I didn't want to bungle it. Ideally this would be the best solution as one could easily apply a dab of silicone on the ends to keep them from moving and not affecting the flow of water with a silicone blob.

This solved my problems. I now periodically inspect the seals to make sure they are still where they should be. Good luck and I hope this helps many.